rs10890920

chr11-109002392-G-Achr11-109002392-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.487 in 152,118 control chromosomes in the GnomAD database, including 19,571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.49 (19567 hom., cov: 33)
  • Exomes 𝑓: 0.65 (4 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73996 AN: 151980 Hom.: 19558 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.650 AC: 13 AN: 20 Hom.: 4 AF XY: 0.611 AC XY: 11 AN XY: 18

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.487 AC: 74023 AN: 152098 Hom.: 19567 Cov.: 33 AF XY: 0.490 AC XY: 36445 AN XY: 74338

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.510

Alfa AF: 0.559 Hom.: 48541

Bravo AF: 0.474

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.77
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10890920; hg19: chr11-108873119;